Mercurial > repos > peterjc > align_back_trans
changeset 2:9fbf29a8c12b draft
v0.0.6 use format_source; v0.0.5 more explicit error msg, citation info
| author | peterjc |
|---|---|
| date | Wed, 05 Aug 2015 10:52:56 -0400 |
| parents | ec202446408a |
| children | de803005027f |
| files | tools/align_back_trans/README.rst tools/align_back_trans/align_back_trans.py tools/align_back_trans/align_back_trans.xml tools/align_back_trans/tool_dependencies.xml |
| diffstat | 4 files changed, 62 insertions(+), 44 deletions(-) [+] |
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--- a/tools/align_back_trans/README.rst Wed Jun 04 08:42:23 2014 -0400 +++ b/tools/align_back_trans/README.rst Wed Aug 05 10:52:56 2015 -0400 @@ -1,7 +1,7 @@ Galaxy tool to back-translate a protein alignment to nucleotides ================================================================ -This tool is copyright 2012-2014 by Peter Cock, The James Hutton Institute +This tool is copyright 2012-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below (MIT licence). @@ -43,11 +43,12 @@ <tool file="align_back_trans/align_back_trans.xml" /> -You will also need to install Biopython 1.62 or later. If you want to run -the unit tests, include this line in ``tools_conf.xml.sample`` and the sample -FASTA files under the ``test-data`` directory. Then:: +You will also need to install Biopython 1.62 or later. - ./run_functional_tests.sh -id align_back_trans +If you wish to run the unit tests, also move/copy the ``test-data/`` files +under Galaxy's ``test-data/`` folder. Then:: + + ./run_tests.sh -id align_back_trans That's it. @@ -63,6 +64,11 @@ v0.0.3 - First official release v0.0.4 - Simplified XML to apply input format to output data. - Fixed error message when sequence length not a multiple of three. +v0.0.5 - More explicit error messages when seqences lengths do not match. + - Tool definition now embeds citation information. +v0.0.6 - Reorder XML elements (internal change only). + - Use ``format_source=...`` tag. + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). ======= ====================================================================== @@ -75,22 +81,31 @@ With the addition of a Galaxy wrapper, developement moved here: https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder:: +For pushing a release to the test or main "Galaxy Tool Shed", use the following +Planemo commands (which requires you have set your Tool Shed access details in +``~/.planemo.yml`` and that you have access rights on the Tool Shed):: + + $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/ + ... + +or:: - $ tar -czf align_back_trans.tar.gz tools/align_back_trans/README.rst tools/align_back_trans/align_back_trans.py tools/align_back_trans/align_back_trans.xml tools/align_back_trans/tool_dependencies.xml test-data/demo_nucs.fasta test-data/demo_nucs_trailing_stop.fasta test-data/demo_prot_align.fasta test-data/demo_nuc_align.fasta + $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/ + ... + +To just build and check the tar ball, use:: -Check this worked:: - - $ tar -tzf align_back_trans.tar.gz + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/align_back_trans/ + ... + $ tar -tzf shed_upload.tar.gz + test-data/demo_nucs.fasta + test-data/demo_nucs_trailing_stop.fasta + test-data/demo_prot_align.fasta + test-data/demo_nuc_align.fasta tools/align_back_trans/README.rst tools/align_back_trans/align_back_trans.py tools/align_back_trans/align_back_trans.xml tools/align_back_trans/tool_dependencies.xml - test-data/demo_nucs.fasta - test-data/demo_nucs_trailing_stop.fasta - test-data/demo_prot_align.fasta - test-data/demo_nuc_align.fasta Licence (MIT)
--- a/tools/align_back_trans/align_back_trans.py Wed Jun 04 08:42:23 2014 -0400 +++ b/tools/align_back_trans/align_back_trans.py Wed Aug 05 10:52:56 2015 -0400 @@ -15,8 +15,6 @@ * http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans See accompanying text file for licence details (MIT licence). - -This is version 0.0.3 of the script. """ import sys @@ -28,10 +26,10 @@ from Bio.Data.CodonTable import ambiguous_generic_by_id if "-v" in sys.argv or "--version" in sys.argv: - print "v0.0.4" + print "v0.0.5" sys.exit(0) -def stop_err(msg, error_level=1): +def sys_exit(msg, error_level=1): """Print error message to stdout and quit with given error level.""" sys.stderr.write("%s\n" % msg) sys.exit(error_level) @@ -39,7 +37,7 @@ def check_trans(identifier, nuc, prot, table): """Returns nucleotide sequence if works (can remove trailing stop)""" if len(nuc) % 3: - stop_err("Nucleotide sequence for %s is length %i (not a multiple of three)" + sys_exit("Nucleotide sequence for %s is length %i (not a multiple of three)" % (identifier, len(nuc))) p = str(prot).upper().replace("*", "X") @@ -49,19 +47,20 @@ #Allow this... t = t[:-1] nuc = nuc[:-3] #edit return value - if len(t) != len(p) and p in t: - stop_err("%s translation matched but only as subset of nucleotides, " - "wrong start codon?" % identifier) - if len(t) != len(p) and p[1:] in t: - stop_err("%s translation matched (ignoring first base) but only " - "as subset of nucleotides, wrong start codon?" % identifier) if len(t) != len(p): - stop_err("Inconsistent lengths for %s, ungapped protein %i, " - "tripled %i vs ungapped nucleotide %i" % - (identifier, - len(p), - len(p) * 3, - len(nuc))) + err = ("Inconsistent lengths for %s, ungapped protein %i, " + "tripled %i vs ungapped nucleotide %i." % + (identifier, len(p), len(p) * 3, len(nuc))) + if t.endswith(p): + err += "\nThere are %i extra nucleotides at the start." % (len(t) - len(p)) + elif t.startswith(p): + err += "\nThere are %i extra nucleotides at the end." % (len(t) - len(p)) + elif p in t: + #TODO - Calculate and report the number to trim at start and end? + err += "\nHowever, protein sequence found within translated nucleotides." + elif p[1:] in t: + err += "\nHowever, ignoring first amino acid, protein sequence found within translated nucleotides." + sys_exit(err) if t == p: @@ -71,7 +70,7 @@ if str(nuc[0:3]).upper() in ambiguous_generic_by_id[table].start_codons: return nuc else: - stop_err("Translation check failed for %s\n" + sys_exit("Translation check failed for %s\n" "Would match if %s was a start codon (check correct table used)\n" % (identifier, nuc[0:3].upper())) else: @@ -86,7 +85,7 @@ sys.stderr.write("Protein: %s\n" % p[offset:offset+60]) sys.stderr.write(" %s\n" % m[offset:offset+60]) sys.stderr.write("Translation: %s\n\n" % t[offset:offset+60]) - stop_err("Translation check failed for %s\n" % identifier) + sys_exit("Translation check failed for %s\n" % identifier) def sequence_back_translate(aligned_protein_record, unaligned_nucleotide_record, gap, table=0): #TODO - Separate arguments for protein gap and nucleotide gap? @@ -107,7 +106,7 @@ if table: ungapped_nucleotide = check_trans(aligned_protein_record.id, ungapped_nucleotide, ungapped_protein, table) elif len(ungapped_protein) * 3 != len(ungapped_nucleotide): - stop_err("Inconsistent lengths for %s, ungapped protein %i, " + sys_exit("Inconsistent lengths for %s, ungapped protein %i, " "tripled %i vs ungapped nucleotide %i" % (aligned_protein_record.id, len(ungapped_protein), @@ -160,7 +159,7 @@ elif len(sys.argv) == 6: align_format, prot_align_file, nuc_fasta_file, nuc_align_file, table = sys.argv[1:] else: - stop_err("""This is a Python script for 'back-translating' a protein alignment, + sys_exit("""This is a Python script for 'back-translating' a protein alignment, It requires three, four or five arguments: - alignment format (e.g. fasta, clustal), @@ -185,7 +184,7 @@ try: table = int(table) except: - stop_err("Bad table argument %r" % table) + sys_exit("Bad table argument %r" % table) prot_align = AlignIO.read(prot_align_file, align_format, alphabet=generic_protein) nuc_dict = SeqIO.index(nuc_fasta_file, "fasta")
--- a/tools/align_back_trans/align_back_trans.xml Wed Jun 04 08:42:23 2014 -0400 +++ b/tools/align_back_trans/align_back_trans.xml Wed Aug 05 10:52:56 2015 -0400 @@ -1,18 +1,18 @@ -<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.4"> +<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.6"> <description>Gives a codon aware alignment</description> <requirements> <requirement type="package" version="1.63">biopython</requirement> <requirement type="python-module">Bio</requirement> </requirements> - <version_command interpreter="python">align_back_trans.py --version</version_command> - <command interpreter="python"> -align_back_trans.py $prot_align.ext "$prot_align" "$nuc_file" "$out_nuc_align" "$table" - </command> <stdio> <!-- Anything other than zero is an error --> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> + <version_command interpreter="python">align_back_trans.py --version</version_command> + <command interpreter="python"> +align_back_trans.py $prot_align.ext "$prot_align" "$nuc_file" "$out_nuc_align" "$table" + </command> <inputs> <param name="prot_align" type="data" format="fasta,muscle,clustal" label="Aligned protein file" help="Mutliple sequence file in FASTA, ClustalW or PHYLIP format." /> <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons"> @@ -38,7 +38,7 @@ <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" /> </inputs> <outputs> - <data name="out_nuc_align" format="input" metadata_source="prot_align" label="${prot_align.name} (back-translated)"/> + <data name="out_nuc_align" format_source="prot_align" metadata_source="prot_align" label="${prot_align.name} (back-translated)"/> </outputs> <tests> <test> @@ -122,4 +122,8 @@ This tool is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans </help> + <citations> + <citation type="doi">10.7717/peerj.167</citation> + <citation type="doi">10.1093/bioinformatics/btp163</citation> + </citations> </tool>
--- a/tools/align_back_trans/tool_dependencies.xml Wed Jun 04 08:42:23 2014 -0400 +++ b/tools/align_back_trans/tool_dependencies.xml Wed Aug 05 10:52:56 2015 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="biopython" version="1.63"> - <repository changeset_revision="a5c49b83e983" name="package_biopython_1_63" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a5c49b83e983" name="package_biopython_1_63" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>